African Journal of Biotechnology Vol. 11(25), pp. 6763-6768, 27 March, 2012 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB11.3099 ISSN 1684–5315 © 2012 Academic Journals
Full Length Research Paper
Isolation, characterization, and hydrolytic activities of Geobacillus species from Jordanian hot springs Maher Obeidat1*, Hala Khyami-Horani2, Adeeb Al-Zoubi3 and Ismael Otri1 1
Department of Biotechnology, Faculty of Agricultural Technology, Balqa’ Applied University, 19117, Al-Salt, Jordan. 2 Department of Biological Sciences, Faculty of Science, University of Jordan, Amman 11942, Jordan. 3 Regenerative Medicine at the University of Illinois, USA. Accepted 28 February, 2012
The present study was conducted to isolate, identify, characterize and to determine the enzymatic activities of the thermophilic Geobacillus species from five Jordanian hot springs. Based on phenotypic characters, eight thermophilic isolates were identified and belonged to the genus Geobacillus. The Geobacillus isolates were abundant in all investigated hot springs. The optimal temperature for growth of the isolates was 60 to 65°C and the optimal pH was 6 to 8. Colonies were light yellow circular to rhizoid. The bacterial cells were Gram positive rods and endospore forming. All isolates produced amylase, caseinase, alkaline and acid phosphatases, esterase (C4), esterase lipase (C8), αGalactosidase, β-Glucuronidase, β-Glucosidase, and N-Acetyl-β-glucosaminidase. Seven isolates produced leucine and valine arylamidases and five isolates produced naphthol-AS-B1phsphohydrolase. Lipase (C14) activity from two isolates and α-chymotrypsin activity from three isolates were also detected. The phenotypic characterization of those isolates was confirmed by genotypic method using 16S rDNA sequence analysis. Maximal homology of all eight isolates to genus Geobacillus was observed. Five of these isolates showed greater than 98% homology with Geobacillus stearothermophilus and one isolate showed 100% homology with Geobacillus thermoglucosidasius. Therefore, 16S rRNA gene sequence analysis can be considered as a valuable genotypic tool for the identification and characterization of thermophilic bacteria at genus level. Moreover, enzymatic products of those isolates could receive considerable attention due to their potential applications in biotechnology. Keywords: Thermophiles, Geobacillus, hydrolytic enzymes, hot spring, 16S rRNA. INTRODUCTION Microorganisms occupy all possible environments including habitats offering ideal conditions for growth and extreme environments. Extremophiles, thermophiles in particular, are getting recognition mainly due to their attractive attributes in biotechnology. The discovery of different life forms at elevated temperatures and the isolation of Thermus aquaticus bacterium producing Taq DNA polymerase, which has a commercial success because of its uses in polymerase chain reaction (PCR) technology, led scientists to isolate and identify
*Corresponding author. E-mail:
[email protected]. Tel: +962775609847. Fax: +96253530469.
microorganisms from the worldwide geothermal sources. Thermophilic microorganisms are adapted to grow at high temperatures and they are separated into three categories; moderate thermophiles, extreme thermophiles and hyperthermophiles (Baker et al., 2001; Bertoldo and Antranikian, 2002). Thus, they can be isolated from high temperature terrestrial and marine habitats including volcanically and geothermally heated hydrothermal vent systems (Bertoldo and Antranikian, 2002). Interest in thermophilic bacteria from the genus Bacillus has clearly emerged during the past two decades because of their significant potential for biotechnological applications including their importance as sources of thermostable enzymes (such as proteases, amylases,
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lipases, xylanases, cellulases and DNA restriction endonucleases), and other products of industrial interest (Bergquist and Morgan, 1992; Maugeri et al., 2001; Rainey et al., 1994; Sharp et al., 1992). Thermophilic bacilli grow best at temperatures between 45 and 70°C, and were isolated from different environments including hot springs, petroleum reservoirs, deep-sea hydrothermal vents and deep ocean-basin cores (Bae et al., 2005; Rahman et al., 2004). Recently, Nazina et al. (2001) grouped Gram positive, rod-shaped, endospore-forming thermophilic bacilli into the genus Geobacillus. The Geobacillus species are widely distributed and readily isolated from different habitats (Meintanis et al., 2006; Nazina et al., 2001), with a continually increasing industrial interest for their thermostable gene products (Lama et al., 2004; Schallmey et al., 2004). Therefore, studying phylogenetic relations and diversity in this novel bacterial genus is not only a taxonomical concern, but also a necessity in order to exploit its biotechnological potential completely. Jordan has a unique location which is rich and diverse extreme environments including the hypersaline Dead Sea, the lowest place on earth, in addition to hot springs. Therefore, the aim of the current study was to isolate, identify and characterize thermophilic Geobacillus bacteria from five hot springs in Jordan using phenotypic (morphological, biochemical and physiological characters) and genotypic methods (16S rRNA gene sequencing). Moreover, the hydrolytic activities of the obtained isolates were also identified. MATERIALS AND METHODS
Genomic DNA extraction Thermophilic bacterial cultures which were thought to belong to Geobacillus and the reference strain Geobacillus stearothermophilus derived from ATCC 7953 were inoculated into 20 ml of Luria Bertani (LB) broth and incubated at 150 rpm overnight at 60°C. Cultures were centrifuged at 14000 rpm for 5 min, cell pellets were washed two times with distilled water, then used for DNA isolation using Wizard Genomic DNA purification kit (Promega, USA, part no. A1120) according to the manufacturer's instructions. Genomic DNA from overnight culture of Escherichia coli ATCC 25922 was also extracted by the kit. PCR amplification of the 16S rRNA gene The PCR amplification of the 16S rRNA genes from purified genomic DNA was performed according to Belduz et al. (2003) by using the forward primer UNI16S-L (5′-ATTCTAGAGTTTGATCATGGCTCA-3′) corresponding to positions 11 to 26 of E. coli 16S rRNA and the reverse primer UNI16S-R (5′-ATGGTACCGTGTGACGGGCGGTGTGTA-3′) corresponding to the complement of positions 1411 to 1393 of E. coli 16S rRNA. PCR reaction conditions were carried out according to Beffa et al. (1996). Sequencing analysis The sequences of 16S rRNA gene from PCR products of the thermophilic isolates, the reference strain G. stearothermophilus ATCC 7953 and E. coli ATCC 25922 were determined with an Applied Biosystems model 373A DNA sequencer by using the ABI PRISM cycle sequencing kit (Macrogen, Korea). The sequences were compared with those contained in the GenBank (Benson et al., 1999) by using a basic local alignment tool (BLAST) search (Altschul et al., 1990). The most closely related 16S rRNA gene sequences to our isolates were retrieved from the database. Retrieved sequences were then aligned and the phylogenetic tree was constructed by the use of DNAMAN 5.2.9 sequence analysis software. E. coli ATCC 25922 was used as the outgroup in the tree.
Isolation of bacteria Water samples were collected from five main hot springs located in different areas in Jordan using 500 ml sterile thermal glass containers. The samples were collected under 40 cm below the surface away from the margin. Water samples were filtered through 0.45 µm membrane filter. The filtrate was re-suspended in 10 ml of sterile sample water. From each sample, 100 µl aliquot was plated by spreading on nutrient agar plates (five replicates) and incubated for 24 h at 50°C. Different colonies were selected and purified by subculturing, and then, were stored in nutrient broth containing 20% glycerol at -80°C until was used.
Phenotypic and physiological characterization of isolates Colony and cell morphology were performed according to the standard protocols. The presence of catalase, oxidase, amylase and caseinase were investigated for each isolate (Harley and Prescott, 2002). In addition, several enzymatic activities of the isolates were determined by API-ZYM system (BioMerieux, USA). Optimal growth temperature was determined by incubating the isolates in nutrient broth medium at 30 to 80°C with 5°C interval. Optimal pH was tested in the range 4.0 to 12.0 in nutrient broth medium with an interval of 0.5 units. The effect of NaCl on the thermophilic bacteria growth was studied by incubating the bacterial isolates in nutrient broth medium containing 0.0 to 10% with 0.5% interval.
RESULTS In the present study, the occurrence of thermophilic bacteria belonging to the genus Geobacillus was investigated in five main hot springs in Jordan (Table 1). The water temperatures ranged from 42.1 to 62.3°C, with pH ranging from 6.0 to 7.0. The highest viable total bacterial count (>400 cfu/ml) was found in Jordan-Himma and Ma`in-Romman Bath, whereas the lowest count (11.4 CFU/ml) was observed in Hammat Afra. Table 1 shows that Geobacillus was abundant (264 CFU/ml) in waters of Jordan-Himma constituting 53.2% of the total viable bacterial count. Whereas, Shuna-North had the lowest content (0.8 CFU/ml) of Geobacillus with a 3.2% of the total viable bacterial count. Out of 36 bacterial isolates from hot springs, 20 were thermophilic (Table 2). Based on morphological, physiological, and biochemical properties (Table 3), eight isolates (JTA1, JTH1, JTS1, JTZ1, JTZ5, JTM1, JTM5, and JTM8) met the criteria of the thermophilic genus Geobacillus. Colonies were light yellow circular to rhizoid on nutrient agar; cells were Gram positive, rod-shaped arranged in single or short chains, motile and endospore-
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Table 1. Abundance and diversity of thermophilic Geobacillus species in Jordanian thermal vents.
Water temperature (°C) 48.2 42.1 54.5 54.1 62.3
Thermal vent Hammat Afra Jordan Himma Shuna-North Zara-Bani Hamida Ma`in-Roman Bath
Water pH 6.5 7.0 6.6 6.3 6.0
Total bacterial a CFU / ml 11.4 496 24.8 342 429
Geobacillus CFU/ml (%) 3.2 (28.1) 264 (53.2) 0.8 (3.2) 60 (17.5) 119 (27.7)
a
CFU, Colony forming unit. The CFU/ml values for total bacteria and Geobacillus were calculated after incubation of nutrient agar plates (five replicates) at 50°C for 24 h.
Table 2. Recovery of thermophilic Geobacillus from different Jordanian thermal vents.
Thermal vent Hammat Afra Jordan Himma Shuna-North Zara-Bani Hamida Ma`in-Roman Bath Total
No. of bacterial isolates 4 6 5 10 11 36
No. of thermophilic isolates (%) 1 (25.0) 2 (33.3) 3 (60.0) 7 (70.0) 7 (63.6) 20 (55.6)
No. of Geobacillus isolates (%) 1 (100) 1 (50.0) 1 (33.3) 2 (28.6) 3 (42.9) 8 (40)
Isolates code JTA1 JTH1 JTS1 JTZ1, JTZ5 JTM1, JTM5, JTM8
Table 3. Growth characteristics and enzymatic activity of thermophilic Geobacillus isolates.
Geobacillus isolate
JTA1
Temperature (optimum)
40-85 (65)
pH (optimum) NaCl % Catalase Oxidaes Amylase Caseinase API ZYM Alkaline phosphatase Esterase (C4) Esterase Lipase (C8) Lipase (C14) Leucine arylamidase Valine arylamidase Cystine arylamidase Trypsin α-Chymotrypsin Acid phosphatase Naphthol-AS-B1phosphohydrolase α-Galactosidase β-Galactosidase β-Glucuronidase α-Glucosidase β-Glucosidase N-Acetyl-β-glucosaminidase α-Mannosidase β-Fucosidase
4-11 (6-8) 0-4% + + + +
JTH1 40-80 (60) 6-9 (6-8) 0-4% + + + +
JTS1
JTZ1
4-11 (6-8) 0-4% + + + +
JTZ5 40-80 (60) 6-9 (7-8) 0-4% + + + +
JTM1 40-80 (60) 6-9 (6-8) 0-4% + + + +
JTM5 40-85 (65) 4-11 (6-8) 0-4% + + + +
JTM8 40-85 (65) 4-11 (6-8) 0-4% + + + +
40-80 (60)
40-85 (65)
6-9 (6-8) 0-4% + + + +
+ + + + + + + +
+ + + + + + +
+ + + + + + +
+ + + +
+ + + + + +
+ + + + + +
+ + + + + +
+ + + + + + +
-
-
+
+
+
-
+
+
+ + + + -
+ + + + -
+ + + + -
+ + + + -
+ + + + -
+ + + + -
+ + + + -
+ + + + -
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Table 4. The comparison of the 16S rDNA gene sequences of the obtained Geobacillus isolates with the 16S rDNA gene sequences in the GenBank.
Sequence a
Geobacillus Isolate
Closest phylogenetic relative (GenBank accession No.)
No. of nucleotidesb
% identityc
JTA1
1388
96
Geobacillus sp. RSNPB7 (HM588147)
JTH1
1377
96
Geobacillus sp. RSNPB7 (HM588147)
JTS1
1353
100
G. thermoglucosidasius (ADNQ01000070)
JTZ1
1387
96
Geobacillus sp. RSNPB7 (HM588147)
JTZ5
1033
95
G. kaustophilus (NC006510)
JTM1
1374
97
Geobacillus sp. RSNPB7 (HM588147)
JTM5
1374
96
Geobacillus sp. RSNPB7 (HM588147)
JTM8
1487
95
G. stearothermophilus WCH1 (HQ143640)
G.s. ATCC
7953
97
a
Geobacillus sp. RSNPB7 (HM588147) b
c
G.s. ATCC is the reference strain G. stearothermophilus ATCC 7953. The number of 16S rDNA nucleotides used for the alignment. The percentage identity with the 16S rDNA sequence of the closest phylogenetic relative of thermophiles.
forming. Optimal temperature was 60 to 65°C and optimal pH was 6 to 8 (Table 3). All isolates were able to grow within the range of 0-4% salt concentration. All isolates produced catalase, oxidase, amylase, caseinase, alkaline and acid phosphatases, esterase (C4), esterase lipase (C8), α-Galactosidase, β-Glucuronidase, β-Glucosidase, and N-Acetyl-β-glucosaminidase (Table 3). Most of the isolates produced leucine arylamidase, valine arylamidase, naphthol-AS-B1-phsphohydrolase. Only one isolate (JTZ1) did not show leucine and valine arylamidases activity and three isolates (JTA1, JTH1, and JTM1) did not show naphthol-AS-B1-phosphohydrolase activity. Lipase (C14) was produced only from two isolates (JTA1 and JTM8) and α-chymotrypsin activity was observed in three isolates (JTA1, JTH1, and JTS1). 16S rRNA gene sequence of the isolates and the reference strain G. stearothermophilus ATCC 7953 was analyzed. The 16S rDNA of the isolates was amplified with UNI16S-L and UNI16S-R primers. The amplified genomic DNA of the isolates and the reference strain produced PCR band with about 1400 bp in size. Based on BLAST alignment of GenBank sequences to 16S rDNA sequences, all eight isolates belonged to genus Geobacillus with 95 to 100% identity (Table 4). The phylogenetic analysis of the 16S rDNA sequences reflected the affiliation of the isolates with the genus Geobacillus and showed that five isolates (JTA1, JTH1, JTZ1, JTM1, and JTM5) appeared closely related to the reference strain (G. stearothermophilus ATCC 7953) with 98.9 to 100% homology and one isolate (JTM8) had 95.8% homology with G. stearothermophilus WCH1 (HQ143640) (Figure 1 and Table 5). Whereas, JTS1 and JTZ5 isolates showed 100 and 95.7% homology with Geobacillus thermoglucosidasius (ADNQ01000070) and Geobacillus kaustophilus (NC006510), respectively.
DISCUSSION A total of 20 thermophilic bacterial isolates were isolated from five hot springs in Jordan. Based on the phenotypic and physiological properties such as occurrence of endospores, production of enzymes and growth at high temperature, a total of eight isolates appeared to be closer to the genus Geobacillus. In terms of phenotypic and physiological characters, the identification of those isolates as Geobacillus species is in agreement with findings of previous studies (Ezeji et al., 2005; Fortina et al., 2001; Nazina et al., 2001, 2004; Romano et al., 2005). The 16S rDNAs of the isolates and one reference strain (G. stearothermophilus ATCC 7953) were sequenced. Therefore, the preliminary identification of the obtained bacterial isolates by conventional methods was confirmed by comparing the 16S rDNA sequences of the isolates with those in the GenBank. As a result, the sequences of the obtained isolates in this study showed 95.7 to 100% sequence homology to the genus Geobacillus. These results are consistent with Nazina et al. (2001), who reported that members of the genus Geobacillus have more than 96% sequence homology. Considering phylogenetic analysis using 16S rDNA, it was revealed that five Geobacillus isolates could be allocated into the species stearothermophilus with homology values ranging between 98.9 to 100%. Moreover, the isolate JTM8 had the highest homology (95.7%) with the species stearothermophilus. On the other hand, JTS1 and JTZ5 isolates could be allocated into the species thermoglucosidasius (100% homology) and kaustophilus (95.7% homology). However, this needs to be further confirmed by fatty acid analysis, DNA hybridization and other techniques. While these results are important for
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Figure 1. Phylogenetic tree showing the relationships between the 16S rDNA sequences of the eight Geobacillus isolates, the reference strain G. stearothermophilus ATCC 7953 and other related Geobacillus sequences previously published in the database. The accession numbers are given in parentheses. The phylogenetic tree was built by the neighbor-joining method, using maximum likelihood parameter distance from the partial 16S rDNA sequences. E. coli (ATCC 25922) was used as the outgroup.
Table 5. Homology matrix shared between Jordanian Geobacillus isolates, the reference strain G. stearothermophilus ATCC 7953, and other related Geobacillus sequences previously published in the database.
Isolatea 2 3 4 5 6 7 8 9 10 11 12 13 14
1 92.1% 99.6% 99.3% 94.5% 98.5% 94.3% 100% 100% 92.7% 92.5% 92.2% 98.3% 95.2%
2
3
4
5
6
7
8
9
10
11
12
92.5% 92.5% 92.1% 92.1% 95.0% 92.1% 92.1% 100% 96.9% 97.2% 91.6%2 92.1%
99.3% 94.5% 99.6% 95.2% 99.6% 99.6% 92.9% 93.2% 92.9% 97.9% 95.7%
96.1% 98.2% 95.7% 99.3% 99.3% 92.7% 92.3% 92.2% 97.6% 96.8%
93.7% 93.4% 94.5% 94.2% 91.8% 91.3% 91.5% 94.3% 95.8%
94.3% 98.5% 98.9% 91.5% 91.3% 91.3% 96.8% 95.2%
94.3% 94.3% 95.0% 95.7% 95.5% 93.9% 94.6%
100% 92.7% 92.5% 92.2% 98.3% 95.2%
92.7% 92.5% 92.2% 98.3% 95.2%
97.1% 97.2% 91.9% 92.8%
98.8% 91.6% 93.1%
91.4% 92.8%
13
95.2%
a
1, JTH1; 2, JTS1; 3, JTM1; 4, JTM5; 5, JTM8; 6, JTZ1; 7, JTZ5; 8, JTA1; 9, G. stearothermophilus ATCC 7953; 10, G. thermoglucosidasius (ADNQ01000070); 11, G. kaustophilus (NC006510); 12, G. thermodenitrificans (NC009328); 13, Geobacillus sp. RSNPB7 (HM588147); and 14, G. stearothermophilus WCH1 (HQ143640).
further taxonomic work, positive results on several enzymes such as amylase, caseinase, lipase, phosphatases and arylamidases of most isolates as well as chymotrypsin activity in some isolates are indication of potential applications of these bacterial products in biotechnology. Therefore, those isolates could receive considerable attention mainly due to the production of industrially important enzymes. It was clearly observed that all Jordanian hot springs investigated in this study were found rich in Geobacillus
species. This richness could be correlated to the environmental conditions and the nutritional status available for growth of Geobacillus in waters of such hot springs. ACKNOWLEDGEMENTS The authors are grateful to the Scientific Research Support Fund / Ministry of Higher Education of Jordan for
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